FMO DATABASE

FMODB ID: GV511

Calculation Name: 1Z0A-C-Xray547

Preferred Name: Ras-related protein Rab-2A

Target Type: SINGLE PROTEIN

Ligand Name: guanosine-5'-diphosphate | magnesium ion

Ligand 3-letter code: GDP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1Z0A

Chain ID: C

ChEMBL ID: CHEMBL4105893

UniProt ID: P61019

Base Structure: X-ray

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Homology Modeling
Water	No
Procedure	Manual calculation
Remarks	ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	169
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-1822417.274133
FMO2-HF: Nuclear repulsion	1754925.847915
FMO2-HF: Total energy	-67491.426218
FMO2-MP2: Total energy	-67689.068048

3D Structure Molmil

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)

Summations of interaction energy for fragment #1(A:2:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-11.769	-9.599	0.119	-0.812	-1.478	-0.002

Interaction energy analysis for fragmet #1(A:2:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.864 / q_NPA : 0.922

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	4	ALA	0	0.049	0.036	3.754	-1.053	0.298	-0.003	-0.587	-0.762	0.000
52	A	53	LYS	1	0.835	0.927	2.859	43.219	43.990	0.123	-0.223	-0.672	-0.002
53	A	54	GLN	0	-0.011	-0.006	5.115	7.107	7.155	-0.001	-0.002	-0.044	0.000
4	A	5	TYR	0	0.032	0.020	5.296	-0.874	-0.874	0.000	0.000	0.000	0.000
5	A	6	LEU	0	-0.022	-0.008	9.509	0.885	0.885	0.000	0.000	0.000	0.000
6	A	7	PHE	0	0.025	0.011	11.856	0.465	0.465	0.000	0.000	0.000	0.000
7	A	8	LYS	1	0.826	0.927	15.849	13.176	13.176	0.000	0.000	0.000	0.000
8	A	9	TYR	0	0.008	-0.025	17.444	-0.088	-0.088	0.000	0.000	0.000	0.000
9	A	10	ILE	0	-0.027	-0.010	21.741	0.228	0.228	0.000	0.000	0.000	0.000
10	A	11	ILE	0	0.001	0.019	25.572	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	12	ILE	0	0.029	0.034	28.093	0.272	0.272	0.000	0.000	0.000	0.000
12	A	13	GLY	0	0.078	0.042	31.158	-0.063	-0.063	0.000	0.000	0.000	0.000
13	A	14	ASP	-1	-0.750	-0.830	34.454	-7.878	-7.878	0.000	0.000	0.000	0.000
14	A	15	THR	0	0.033	0.011	37.030	-0.179	-0.179	0.000	0.000	0.000	0.000
15	A	16	GLY	0	0.042	0.013	38.855	0.088	0.088	0.000	0.000	0.000	0.000
16	A	17	VAL	0	-0.041	-0.016	34.034	0.080	0.080	0.000	0.000	0.000	0.000
17	A	18	GLY	0	0.024	0.015	34.224	-0.116	-0.116	0.000	0.000	0.000	0.000
18	A	19	LYS	1	0.778	0.879	30.984	8.781	8.781	0.000	0.000	0.000	0.000
19	A	20	SER	0	0.098	0.045	30.006	-0.343	-0.343	0.000	0.000	0.000	0.000
20	A	21	CYS	-1	-0.892	-0.933	30.517	-9.325	-9.325	0.000	0.000	0.000	0.000
21	A	22	LEU	0	-0.027	-0.022	27.612	-0.242	-0.242	0.000	0.000	0.000	0.000
22	A	23	LEU	0	-0.006	0.005	24.891	-0.505	-0.505	0.000	0.000	0.000	0.000
23	A	24	LEU	0	-0.003	0.005	25.939	-0.402	-0.402	0.000	0.000	0.000	0.000
24	A	25	GLN	0	-0.009	-0.018	27.380	-0.446	-0.446	0.000	0.000	0.000	0.000
25	A	26	PHE	0	0.003	0.003	18.078	-0.441	-0.441	0.000	0.000	0.000	0.000
26	A	27	THR	0	-0.076	-0.067	22.223	-0.609	-0.609	0.000	0.000	0.000	0.000
27	A	28	ASP	-1	-0.822	-0.890	23.267	-11.760	-11.760	0.000	0.000	0.000	0.000
28	A	29	LYS	1	0.836	0.937	21.045	13.726	13.726	0.000	0.000	0.000	0.000
29	A	30	ARG	1	0.837	0.913	27.013	10.607	10.607	0.000	0.000	0.000	0.000
30	A	31	PHE	0	0.031	0.017	30.677	-0.020	-0.020	0.000	0.000	0.000	0.000
31	A	32	GLN	0	0.026	-0.004	33.371	-0.035	-0.035	0.000	0.000	0.000	0.000
32	A	33	PRO	0	-0.010	0.015	36.186	-0.088	-0.088	0.000	0.000	0.000	0.000
33	A	34	VAL	0	-0.040	-0.024	37.223	0.225	0.225	0.000	0.000	0.000	0.000
34	A	35	HIS	0	-0.045	-0.031	36.115	0.020	0.020	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.901	-0.935	37.464	-7.974	-7.974	0.000	0.000	0.000	0.000
36	A	37	LEU	0	-0.022	-0.020	35.000	-0.225	-0.225	0.000	0.000	0.000	0.000
37	A	38	THR	0	0.008	0.018	34.997	0.265	0.265	0.000	0.000	0.000	0.000
38	A	39	ILE	0	-0.003	-0.023	34.854	-0.282	-0.282	0.000	0.000	0.000	0.000
39	A	40	GLY	0	-0.018	0.002	33.382	0.088	0.088	0.000	0.000	0.000	0.000
40	A	41	VAL	0	-0.075	-0.047	30.892	-0.326	-0.326	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.831	-0.898	30.646	-9.793	-9.793	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.034	-0.032	21.729	-0.504	-0.504	0.000	0.000	0.000	0.000
43	A	44	GLY	0	0.050	0.034	24.298	0.246	0.246	0.000	0.000	0.000	0.000
44	A	45	ALA	0	-0.055	-0.032	19.002	-0.471	-0.471	0.000	0.000	0.000	0.000
45	A	46	ARG	1	0.812	0.886	17.235	15.874	15.874	0.000	0.000	0.000	0.000
46	A	47	MET	0	-0.050	-0.012	10.586	-0.575	-0.575	0.000	0.000	0.000	0.000
47	A	48	ILE	0	0.025	0.017	12.551	1.294	1.294	0.000	0.000	0.000	0.000
48	A	49	THR	0	-0.029	-0.023	8.168	-2.587	-2.587	0.000	0.000	0.000	0.000
49	A	50	ILE	0	0.027	0.021	8.968	2.129	2.129	0.000	0.000	0.000	0.000
50	A	51	ASP	-1	-0.806	-0.879	7.566	-33.374	-33.374	0.000	0.000	0.000	0.000
51	A	52	GLY	0	-0.014	-0.002	6.074	-3.373	-3.373	0.000	0.000	0.000	0.000
54	A	55	ILE	0	0.019	0.002	7.710	-2.277	-2.277	0.000	0.000	0.000	0.000
55	A	56	LYS	1	0.913	0.968	10.379	19.955	19.955	0.000	0.000	0.000	0.000
56	A	57	LEU	0	0.018	0.016	13.598	0.019	0.019	0.000	0.000	0.000	0.000
57	A	58	GLN	0	-0.020	-0.037	16.718	0.318	0.318	0.000	0.000	0.000	0.000
58	A	59	ILE	0	0.004	0.013	19.734	0.036	0.036	0.000	0.000	0.000	0.000
59	A	60	TRP	0	-0.014	-0.001	22.801	0.304	0.304	0.000	0.000	0.000	0.000
60	A	61	ASP	-1	-0.802	-0.923	26.424	-9.778	-9.778	0.000	0.000	0.000	0.000
61	A	62	THR	0	-0.074	-0.070	29.439	0.125	0.125	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.025	-0.005	31.857	0.264	0.264	0.000	0.000	0.000	0.000
63	A	64	GLY	0	0.006	0.000	35.127	-0.048	-0.048	0.000	0.000	0.000	0.000
64	A	65	GLN	0	0.032	0.016	35.180	-0.109	-0.109	0.000	0.000	0.000	0.000
65	A	66	GLU	-1	-0.782	-0.886	37.276	-8.338	-8.338	0.000	0.000	0.000	0.000
66	A	67	SER	0	-0.043	-0.011	39.464	0.040	0.040	0.000	0.000	0.000	0.000
67	A	68	PHE	0	-0.030	-0.021	40.637	0.187	0.187	0.000	0.000	0.000	0.000
68	A	69	ARG	1	0.786	0.879	38.338	7.531	7.531	0.000	0.000	0.000	0.000
69	A	70	SER	0	-0.028	-0.025	36.373	-0.089	-0.089	0.000	0.000	0.000	0.000
70	A	71	ILE	0	-0.014	-0.004	30.049	0.079	0.079	0.000	0.000	0.000	0.000
71	A	72	THR	0	-0.008	-0.011	33.412	0.067	0.067	0.000	0.000	0.000	0.000
72	A	73	ARG	1	0.915	0.936	31.822	8.401	8.401	0.000	0.000	0.000	0.000
73	A	74	SER	0	-0.046	-0.018	29.566	-0.304	-0.304	0.000	0.000	0.000	0.000
74	A	75	TYR	0	0.039	0.024	27.739	-0.509	-0.509	0.000	0.000	0.000	0.000
75	A	76	TYR	0	0.042	-0.025	26.251	-0.722	-0.722	0.000	0.000	0.000	0.000
76	A	77	ARG	1	0.941	0.975	25.622	10.793	10.793	0.000	0.000	0.000	0.000
77	A	78	GLY	0	-0.003	-0.002	22.111	-0.162	-0.162	0.000	0.000	0.000	0.000
78	A	79	ALA	0	-0.048	-0.010	20.873	-0.685	-0.685	0.000	0.000	0.000	0.000
79	A	80	ALA	0	-0.006	-0.003	17.495	0.006	0.006	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.031	0.018	19.606	-0.028	-0.028	0.000	0.000	0.000	0.000
81	A	82	ALA	0	-0.008	-0.017	21.272	0.191	0.191	0.000	0.000	0.000	0.000
82	A	83	LEU	0	-0.009	0.004	22.700	0.093	0.093	0.000	0.000	0.000	0.000
83	A	84	LEU	0	0.006	0.005	26.419	0.280	0.280	0.000	0.000	0.000	0.000
84	A	85	VAL	0	-0.017	-0.016	29.698	0.086	0.086	0.000	0.000	0.000	0.000
85	A	86	TYR	0	0.052	0.011	32.017	0.177	0.177	0.000	0.000	0.000	0.000
86	A	87	ASP	-1	-0.733	-0.833	35.020	-7.989	-7.989	0.000	0.000	0.000	0.000
87	A	88	ILE	0	0.011	0.009	36.120	0.193	0.193	0.000	0.000	0.000	0.000
88	A	89	THR	0	-0.084	-0.058	38.845	0.208	0.208	0.000	0.000	0.000	0.000
89	A	90	ARG	1	0.836	0.913	39.794	7.757	7.757	0.000	0.000	0.000	0.000
90	A	91	ARG	1	0.831	0.880	41.766	6.938	6.938	0.000	0.000	0.000	0.000
91	A	92	ASP	-1	-0.891	-0.951	42.553	-7.055	-7.055	0.000	0.000	0.000	0.000
92	A	93	THR	0	-0.022	-0.022	38.624	-0.163	-0.163	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.029	-0.014	36.645	-0.204	-0.204	0.000	0.000	0.000	0.000
94	A	95	ASN	0	0.001	-0.018	39.248	-0.141	-0.141	0.000	0.000	0.000	0.000
95	A	96	HIS	0	-0.010	0.003	40.778	0.100	0.100	0.000	0.000	0.000	0.000
96	A	97	LEU	0	-0.024	0.003	34.121	-0.168	-0.168	0.000	0.000	0.000	0.000
97	A	98	THR	0	-0.006	-0.013	36.071	-0.226	-0.226	0.000	0.000	0.000	0.000
98	A	99	THR	0	0.030	0.026	37.854	-0.046	-0.046	0.000	0.000	0.000	0.000
99	A	100	TRP	0	0.036	-0.002	33.961	-0.157	-0.157	0.000	0.000	0.000	0.000
100	A	101	LEU	0	-0.039	-0.006	31.819	-0.291	-0.291	0.000	0.000	0.000	0.000
101	A	102	GLU	-1	-0.909	-0.957	33.751	-7.981	-7.981	0.000	0.000	0.000	0.000
102	A	103	ASP	-1	-0.711	-0.812	34.137	-9.258	-9.258	0.000	0.000	0.000	0.000
103	A	104	ALA	0	0.002	-0.003	29.785	-0.190	-0.190	0.000	0.000	0.000	0.000
104	A	105	ARG	1	0.845	0.931	29.418	9.644	9.644	0.000	0.000	0.000	0.000
105	A	106	GLN	0	-0.036	-0.001	32.561	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	107	HIS	0	-0.041	-0.021	32.168	0.129	0.129	0.000	0.000	0.000	0.000
107	A	108	SER	0	-0.049	-0.035	26.893	-0.406	-0.406	0.000	0.000	0.000	0.000
108	A	109	ASN	0	0.018	0.008	23.745	-0.031	-0.031	0.000	0.000	0.000	0.000
109	A	110	SER	0	0.036	0.011	25.297	-0.284	-0.284	0.000	0.000	0.000	0.000
110	A	111	ASN	0	-0.031	-0.016	20.593	-0.149	-0.149	0.000	0.000	0.000	0.000
111	A	112	MET	0	-0.036	0.000	20.977	-0.626	-0.626	0.000	0.000	0.000	0.000
112	A	113	VAL	0	0.024	0.020	19.300	0.513	0.513	0.000	0.000	0.000	0.000
113	A	114	ILE	0	-0.007	-0.005	22.249	0.117	0.117	0.000	0.000	0.000	0.000
114	A	115	MET	0	-0.009	0.019	22.773	0.184	0.184	0.000	0.000	0.000	0.000
115	A	116	LEU	0	-0.037	-0.010	25.610	0.215	0.215	0.000	0.000	0.000	0.000
116	A	117	ILE	0	0.001	-0.021	26.119	-0.148	-0.148	0.000	0.000	0.000	0.000
117	A	118	GLY	0	0.054	0.035	30.158	0.271	0.271	0.000	0.000	0.000	0.000
118	A	119	ASN	0	0.000	-0.012	32.357	-0.186	-0.186	0.000	0.000	0.000	0.000
119	A	120	LYS	1	0.822	0.896	33.664	8.253	8.253	0.000	0.000	0.000	0.000
120	A	121	SER	0	0.050	-0.002	33.491	0.215	0.215	0.000	0.000	0.000	0.000
121	A	122	ASP	-1	-0.875	-0.914	36.137	-8.263	-8.263	0.000	0.000	0.000	0.000
122	A	123	LEU	0	-0.057	-0.032	37.821	0.248	0.248	0.000	0.000	0.000	0.000
123	A	124	GLU	-1	-0.776	-0.864	39.645	-7.521	-7.521	0.000	0.000	0.000	0.000
124	A	125	SER	0	-0.046	-0.026	41.421	0.154	0.154	0.000	0.000	0.000	0.000
125	A	126	ARG	1	0.860	0.914	43.888	6.706	6.706	0.000	0.000	0.000	0.000
126	A	127	ARG	1	0.737	0.828	36.815	7.963	7.963	0.000	0.000	0.000	0.000
127	A	128	GLU	-1	-0.866	-0.920	42.754	-6.656	-6.656	0.000	0.000	0.000	0.000
128	A	129	VAL	0	-0.044	-0.013	38.619	0.073	0.073	0.000	0.000	0.000	0.000
129	A	130	LYS	1	0.883	0.937	39.935	7.228	7.228	0.000	0.000	0.000	0.000
130	A	131	LYS	1	0.912	0.949	31.692	9.147	9.147	0.000	0.000	0.000	0.000
131	A	132	GLU	-1	-0.800	-0.915	35.335	-7.873	-7.873	0.000	0.000	0.000	0.000
132	A	133	GLU	-1	-0.822	-0.865	37.188	-7.307	-7.307	0.000	0.000	0.000	0.000
133	A	134	GLY	0	0.039	0.027	34.440	-0.045	-0.045	0.000	0.000	0.000	0.000
134	A	135	GLU	-1	-0.853	-0.916	31.635	-9.363	-9.363	0.000	0.000	0.000	0.000
135	A	136	ALA	0	-0.028	-0.011	33.075	-0.154	-0.154	0.000	0.000	0.000	0.000
136	A	137	PHE	0	0.041	0.014	33.742	-0.080	-0.080	0.000	0.000	0.000	0.000
137	A	138	ALA	0	0.007	-0.007	29.623	-0.085	-0.085	0.000	0.000	0.000	0.000
138	A	139	ARG	1	0.954	0.977	30.872	8.796	8.796	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.909	-0.940	32.088	-8.131	-8.131	0.000	0.000	0.000	0.000
140	A	141	HIS	1	0.787	0.882	32.844	8.597	8.597	0.000	0.000	0.000	0.000
141	A	142	GLY	0	-0.002	0.017	29.098	-0.150	-0.150	0.000	0.000	0.000	0.000
142	A	143	LEU	0	-0.057	-0.021	26.980	-0.275	-0.275	0.000	0.000	0.000	0.000
143	A	144	ILE	0	0.033	0.029	21.556	0.188	0.188	0.000	0.000	0.000	0.000
144	A	145	PHE	0	0.018	-0.024	25.816	0.266	0.266	0.000	0.000	0.000	0.000
145	A	146	MET	0	-0.030	-0.002	24.801	-0.409	-0.409	0.000	0.000	0.000	0.000
146	A	147	GLU	-1	-0.769	-0.846	28.383	-8.375	-8.375	0.000	0.000	0.000	0.000
147	A	148	THR	0	0.027	0.001	27.766	-0.230	-0.230	0.000	0.000	0.000	0.000
148	A	149	SER	0	-0.091	-0.048	30.615	0.365	0.365	0.000	0.000	0.000	0.000
149	A	150	ALA	0	0.042	0.017	30.507	-0.183	-0.183	0.000	0.000	0.000	0.000
150	A	151	LYS	1	0.927	0.975	31.578	7.718	7.718	0.000	0.000	0.000	0.000
151	A	152	THR	0	-0.010	-0.031	33.081	0.004	0.004	0.000	0.000	0.000	0.000
152	A	153	ALA	0	0.030	0.026	27.535	-0.112	-0.112	0.000	0.000	0.000	0.000
153	A	154	SER	0	0.007	0.013	27.685	-0.479	-0.479	0.000	0.000	0.000	0.000
154	A	155	ASN	0	0.009	-0.016	26.146	-0.067	-0.067	0.000	0.000	0.000	0.000
155	A	156	VAL	0	0.017	0.016	25.023	-0.245	-0.245	0.000	0.000	0.000	0.000
156	A	157	GLU	-1	-0.787	-0.878	19.537	-15.128	-15.128	0.000	0.000	0.000	0.000
157	A	158	GLU	-1	-0.861	-0.941	20.525	-13.028	-13.028	0.000	0.000	0.000	0.000
158	A	159	ALA	0	0.036	0.014	21.165	-0.417	-0.417	0.000	0.000	0.000	0.000
159	A	160	PHE	0	0.011	0.009	19.606	-0.292	-0.292	0.000	0.000	0.000	0.000
160	A	161	ILE	0	0.004	0.004	15.667	-0.881	-0.881	0.000	0.000	0.000	0.000
161	A	162	ASN	0	-0.008	-0.023	16.569	-1.322	-1.322	0.000	0.000	0.000	0.000
162	A	163	THR	0	-0.004	-0.006	18.604	0.038	0.038	0.000	0.000	0.000	0.000
163	A	164	ALA	0	-0.024	-0.012	13.856	-0.380	-0.380	0.000	0.000	0.000	0.000
164	A	165	LYS	1	0.918	0.963	14.069	15.869	15.869	0.000	0.000	0.000	0.000
165	A	166	GLU	-1	-0.881	-0.937	15.120	-14.547	-14.547	0.000	0.000	0.000	0.000
166	A	167	ILE	0	-0.067	-0.049	14.506	0.103	0.103	0.000	0.000	0.000	0.000
167	A	168	TYR	0	-0.162	-0.108	7.209	-2.231	-2.231	0.000	0.000	0.000	0.000
168	A	169	GLU	-1	-0.952	-0.991	12.387	-19.649	-19.649	0.000	0.000	0.000	0.000
169	A	170	LYS	0	-0.067	0.000	14.477	-1.044	-1.044	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:ALA)